loading ggplot2 and reticulate causes crash with source_python()

[neurotakuko]

Looking for help for this issue. source_python() works fine if I do not load ggplot2.
If both libraries are loaded, execution of source_python() results in crash "R session Aborted R encountered a fatal error"

library(ggplot2)
library(reticulate)
source_python("loadTDdata.py")

import os
import pandas as pd
import tdt

def loadTDdata_py(filepath):
	data = tdt.read_block(os.path.dirname(filepath))
	FPdata = pd.DataFrame({'f405':data.streams._405A.data, 'f465':data.streams._465A.data})
	return FPdata

[kevinushey]

Easier to run example:

library(ggplot2)
library(reticulate)

pycode <- "
import os
import pandas as pd
import tdt

def loadTDdata_py(filepath):
	data = tdt.read_block(os.path.dirname(filepath))
	FPdata = pd.DataFrame({'f405':data.streams._405A.data, 'f465':data.streams._465A.data})
	return FPdata
"

pyfile <- tempfile(fileext = ".py")
writeLines(pycode, con = pyfile)

source_python(pyfile)

Unfortunately, this works without issue for me so I'm not sure what might be going on.

[neurotakuko]

Ah, sorry about that. Thank you for taking the time to make the easier to run example.

I encounter the crash with your example as well. I'm pretty stuck on how to look further into the problem on my end since the crash means no error text to work with. Earlier today I actually came across your comment (https://community.rstudio.com/t/rstudio-v1-2-1153-1-preview-reticulate-python-failure-in-r-notebook/18956/9) and I was attempting to get set-up with gdb when I realized the macOS debugger is lldb. I'm definitely in over my head with this and I would really be grateful for tips on how to capture the error with lldb.

[neurotakuko]

I was able to locate the following crash report. Any help much appreciated with trying to understand it.

Process:               rsession [59038]
Path:                  /Applications/RStudio.app/Contents/MacOS/rsession
Identifier:            rsession
Version:               ???
Code Type:             X86-64 (Native)
Parent Process:        RStudio [59028]
Responsible:           Terminal [59007]
User ID:               503

Date/Time:             2020-10-29 09:33:43.728 -0500
OS Version:            Mac OS X 10.15.6 (19G2021)
Report Version:        12
Anonymous UUID:        4F22444E-44E5-362E-949E-779D32EDECF5

Sleep/Wake UUID:       32025BED-F706-4107-99BD-B40D60E9748F

Time Awake Since Boot: 460000 seconds
Time Since Wake:       2400 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_CRASH (SIGABRT)
Exception Codes:       0x0000000000000000, 0x0000000000000000
Exception Note:        EXC_CORPSE_NOTIFY

Application Specific Information:
abort() called

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib        	0x00007fff6848d33a __pthread_kill + 10
1   libsystem_pthread.dylib       	0x00007fff6854de60 pthread_kill + 430
2   libsystem_c.dylib             	0x00007fff68414808 abort + 120
3   libomp.dylib                  	0x0000000119bbe69b __kmp_abort_process + 43
4   libomp.dylib                  	0x0000000119bbcdfa __kmp_fatal + 170
5   libomp.dylib                  	0x0000000119bc6385 __kmp_register_library_startup() + 645
6   libomp.dylib                  	0x0000000119bbd4ef __kmp_do_serial_initialize() + 31
7   libomp.dylib                  	0x0000000119bbd4af __kmp_get_global_thread_id_reg + 95
8   libomp.dylib                  	0x0000000119c0f2d9 omp_in_parallel + 9
9   libopenblasp-r0.3.10.dylib    	0x00000001159908cb cblas_dsyrk + 459
10  _multiarray_umath.cpython-36m-darwin.so	0x000000011585280f syrk + 591
11  _multiarray_umath.cpython-36m-darwin.so	0x0000000115852464 cblas_matrixproduct + 4340
12  _multiarray_umath.cpython-36m-darwin.so	0x0000000115680670 PyArray_MatrixProduct2 + 240
13  _multiarray_umath.cpython-36m-darwin.so	0x000000011568bce5 array_matrixproduct + 181
14  libpython3.6m.dylib           	0x0000000115271bdb PyCFunction_Call + 59
15  libpython3.6m.dylib           	0x00000001152129f8 PyObject_Call + 168
16  _multiarray_umath.cpython-36m-darwin.so	0x00000001155c82ba array_implement_array_function + 298
17  libpython3.6m.dylib           	0x00000001152723af _PyCFunction_FastCallDict + 671
18  libpython3.6m.dylib           	0x0000000115324330 call_function + 496
19  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
20  libpython3.6m.dylib           	0x0000000115317cf9 _PyEval_EvalCodeWithName + 3273
21  libpython3.6m.dylib           	0x0000000115324554 fast_function + 356
22  libpython3.6m.dylib           	0x0000000115324309 call_function + 457
23  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
24  libpython3.6m.dylib           	0x0000000115317cf9 _PyEval_EvalCodeWithName + 3273
25  libpython3.6m.dylib           	0x0000000115249681 function_call + 673
26  libpython3.6m.dylib           	0x00000001152129f8 PyObject_Call + 168
27  _multiarray_umath.cpython-36m-darwin.so	0x00000001155c82ba array_implement_array_function + 298
28  libpython3.6m.dylib           	0x00000001152723af _PyCFunction_FastCallDict + 671
29  libpython3.6m.dylib           	0x0000000115324330 call_function + 496
30  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
31  libpython3.6m.dylib           	0x0000000115317cf9 _PyEval_EvalCodeWithName + 3273
32  libpython3.6m.dylib           	0x0000000115324554 fast_function + 356
33  libpython3.6m.dylib           	0x0000000115324309 call_function + 457
34  libpython3.6m.dylib           	0x0000000115320215 _PyEval_EvalFrameDefault + 32709
35  libpython3.6m.dylib           	0x00000001153245f6 fast_function + 518
36  libpython3.6m.dylib           	0x0000000115324309 call_function + 457
37  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
38  libpython3.6m.dylib           	0x0000000115317cf9 _PyEval_EvalCodeWithName + 3273
39  libpython3.6m.dylib           	0x00000001153134b7 builtin_exec + 775
40  libpython3.6m.dylib           	0x0000000115271cdf PyCFunction_Call + 319
41  libpython3.6m.dylib           	0x00000001153204b8 _PyEval_EvalFrameDefault + 33384
42  libpython3.6m.dylib           	0x0000000115317cf9 _PyEval_EvalCodeWithName + 3273
43  libpython3.6m.dylib           	0x0000000115324554 fast_function + 356
44  libpython3.6m.dylib           	0x0000000115324309 call_function + 457
45  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
46  libpython3.6m.dylib           	0x00000001153245f6 fast_function + 518
47  libpython3.6m.dylib           	0x0000000115324309 call_function + 457
48  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
49  libpython3.6m.dylib           	0x00000001153245f6 fast_function + 518
50  libpython3.6m.dylib           	0x0000000115324309 call_function + 457
51  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
52  libpython3.6m.dylib           	0x00000001153245f6 fast_function + 518
53  libpython3.6m.dylib           	0x0000000115324309 call_function + 457
54  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
55  libpython3.6m.dylib           	0x000000011532529e _PyFunction_FastCallDict + 1470
56  libpython3.6m.dylib           	0x000000011520c055 _PyObject_FastCallDict + 245
57  libpython3.6m.dylib           	0x00000001152143ea _PyObject_CallMethodIdObjArgs + 858
58  libpython3.6m.dylib           	0x0000000115344536 PyImport_ImportModuleLevelObject + 1446
59  libpython3.6m.dylib           	0x0000000115312393 builtin___import__ + 147
60  libpython3.6m.dylib           	0x0000000115271bdb PyCFunction_Call + 59
61  libpython3.6m.dylib           	0x00000001153204b8 _PyEval_EvalFrameDefault + 33384
62  libpython3.6m.dylib           	0x0000000115317cf9 _PyEval_EvalCodeWithName + 3273
63  libpython3.6m.dylib           	0x0000000115324554 fast_function + 356
64  libpython3.6m.dylib           	0x0000000115324309 call_function + 457
65  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
66  libpython3.6m.dylib           	0x00000001153245f6 fast_function + 518
67  libpython3.6m.dylib           	0x0000000115324309 call_function + 457
68  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
69  libpython3.6m.dylib           	0x000000011532529e _PyFunction_FastCallDict + 1470
70  libpython3.6m.dylib           	0x000000011520c055 _PyObject_FastCallDict + 245
71  libpython3.6m.dylib           	0x00000001152143ea _PyObject_CallMethodIdObjArgs + 858
72  libpython3.6m.dylib           	0x0000000115344536 PyImport_ImportModuleLevelObject + 1446
73  libpython3.6m.dylib           	0x0000000115312393 builtin___import__ + 147
74  libpython3.6m.dylib           	0x0000000115271bdb PyCFunction_Call + 59
75  libpython3.6m.dylib           	0x00000001153204b8 _PyEval_EvalFrameDefault + 33384
76  libpython3.6m.dylib           	0x0000000115317cf9 _PyEval_EvalCodeWithName + 3273
77  libpython3.6m.dylib           	0x0000000115324554 fast_function + 356
78  libpython3.6m.dylib           	0x0000000115324309 call_function + 457
79  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
80  libpython3.6m.dylib           	0x00000001153245f6 fast_function + 518
81  libpython3.6m.dylib           	0x0000000115324309 call_function + 457
82  libpython3.6m.dylib           	0x0000000115320179 _PyEval_EvalFrameDefault + 32553
83  libpython3.6m.dylib           	0x000000011532529e _PyFunction_FastCallDict + 1470
84  libpython3.6m.dylib           	0x000000011520c055 _PyObject_FastCallDict + 245
85  libpython3.6m.dylib           	0x00000001152143ea _PyObject_CallMethodIdObjArgs + 858
86  libpython3.6m.dylib           	0x0000000115344536 PyImport_ImportModuleLevelObject + 1446
87  libpython3.6m.dylib           	0x0000000115312393 builtin___import__ + 147
88  libpython3.6m.dylib           	0x0000000115271bdb PyCFunction_Call + 59
89  libpython3.6m.dylib           	0x000000011521343a PyObject_CallFunction + 666
90  libpython3.6m.dylib           	0x0000000115343c69 PyImport_Import + 633
91  libpython3.6m.dylib           	0x0000000115344c5c PyImport_ImportModule + 28
92  reticulate.so                 	0x000000010fa89ab5 libpython::import_numpy_api(bool, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >*) + 37
93  reticulate.so                 	0x000000010fa94bf3 py_initialize(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, bool, bool, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) + 787
94  reticulate.so                 	0x000000010fa734fa _reticulate_py_initialize + 762
95  libR.dylib                    	0x000000010120bc17 R_doDotCall + 2871
96  libR.dylib                    	0x000000010124b49b bcEval + 62859 (eval.c:7289)
97  libR.dylib                    	0x000000010123b7db Rf_eval + 443
98  libR.dylib                    	0x000000010124e14c R_execClosure + 3004
99  libR.dylib                    	0x00000001012407f3 bcEval + 18659 (eval.c:6749)
100 libR.dylib                    	0x000000010123b7db Rf_eval + 443
101 libR.dylib                    	0x000000010124e14c R_execClosure + 3004
102 libR.dylib                    	0x00000001012407f3 bcEval + 18659 (eval.c:6749)
103 libR.dylib                    	0x000000010123b7db Rf_eval + 443
104 libR.dylib                    	0x000000010124c513 forcePromise + 179 (eval.c:520)
105 libR.dylib                    	0x0000000101257106 getvar + 518 (eval.c:5022)
106 libR.dylib                    	0x000000010123efcc bcEval + 12476 (eval.c:6513)
107 libR.dylib                    	0x000000010123b7db Rf_eval + 443
108 libR.dylib                    	0x000000010124c513 forcePromise + 179 (eval.c:520)
109 libR.dylib                    	0x0000000101257106 getvar + 518 (eval.c:5022)
110 libR.dylib                    	0x000000010123efcc bcEval + 12476 (eval.c:6513)
111 libR.dylib                    	0x000000010123b7db Rf_eval + 443
112 libR.dylib                    	0x000000010124c513 forcePromise + 179 (eval.c:520)
113 libR.dylib                    	0x0000000101257106 getvar + 518 (eval.c:5022)
114 libR.dylib                    	0x000000010123efcc bcEval + 12476 (eval.c:6513)
115 libR.dylib                    	0x000000010123b7db Rf_eval + 443
116 libR.dylib                    	0x000000010124c513 forcePromise + 179 (eval.c:520)
117 libR.dylib                    	0x0000000101257106 getvar + 518 (eval.c:5022)
118 libR.dylib                    	0x000000010123efcc bcEval + 12476 (eval.c:6513)
119 libR.dylib                    	0x000000010123b7db Rf_eval + 443
120 libR.dylib                    	0x000000010124e14c R_execClosure + 3004
121 libR.dylib                    	0x00000001012407f3 bcEval + 18659 (eval.c:6749)
122 libR.dylib                    	0x000000010123b7db Rf_eval + 443
123 libR.dylib                    	0x000000010124e14c R_execClosure + 3004
124 libR.dylib                    	0x00000001012407f3 bcEval + 18659 (eval.c:6749)
125 libR.dylib                    	0x000000010123b7db Rf_eval + 443
126 libR.dylib                    	0x000000010124e14c R_execClosure + 3004
127 libR.dylib                    	0x00000001012407f3 bcEval + 18659 (eval.c:6749)
128 libR.dylib                    	0x000000010123b7db Rf_eval + 443
129 libR.dylib                    	0x000000010124e14c R_execClosure + 3004
130 libR.dylib                    	0x00000001012407f3 bcEval + 18659 (eval.c:6749)
131 libR.dylib                    	0x000000010123b7db Rf_eval + 443
132 libR.dylib                    	0x000000010124e14c R_execClosure + 3004
133 libR.dylib                    	0x00000001012407f3 bcEval + 18659 (eval.c:6749)
134 libR.dylib                    	0x000000010123b7db Rf_eval + 443
135 libR.dylib                    	0x000000010124e14c R_execClosure + 3004
136 libR.dylib                    	0x00000001012407f3 bcEval + 18659 (eval.c:6749)
137 libR.dylib                    	0x000000010123b7db Rf_eval + 443
138 libR.dylib                    	0x000000010124e14c R_execClosure + 3004
139 libR.dylib                    	0x00000001012407f3 bcEval + 18659 (eval.c:6749)
140 libR.dylib                    	0x000000010123b7db Rf_eval + 443
141 libR.dylib                    	0x000000010124e14c R_execClosure + 3004
142 libR.dylib                    	0x000000010123bd0c Rf_eval + 1772 (eval.c:747)
143 libR.dylib                    	0x000000010127ebda Rf_ReplIteration + 794 (main.c:258)
144 libR.dylib                    	0x00000001012801bf run_Rmainloop + 207 (main.c:1082)
145 rsession                      	0x00000001008506d9 rstudio::r::session::runEmbeddedR(rstudio::core::FilePath const&, rstudio::core::FilePath const&, bool, bool, SA_TYPE, rstudio::r::session::Callbacks const&, rstudio::r::session::InternalCallbacks*) + 425
146 rsession                      	0x000000010082f6dc rstudio::r::session::run(rstudio::r::session::ROptions const&, rstudio::r::session::RCallbacks const&) + 3164
147 rsession                      	0x0000000100108b63 main + 28963
148 rsession                      	0x00000001000037b4 start + 52

Thread 1:
0   libsystem_kernel.dylib        	0x00007fff68489882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6854e425 _pthread_cond_wait + 698
2   rsession                      	0x000000010001507c bool rstudio_boost::condition_variable_any::do_wait_until<rstudio_boost::unique_lock<rstudio_boost::mutex> >(rstudio_boost::unique_lock<rstudio_boost::mutex>&, timespec const&) + 76
3   rsession                      	0x00000001007795d0 rstudio::core::thread::ThreadsafeQueue<rstudio::core::system::file_monitor::(anonymous namespace)::RegistrationCommand>::wait(rstudio_boost::posix_time::time_duration const&) + 608
4   rsession                      	0x000000010077985c rstudio::core::system::file_monitor::(anonymous namespace)::checkForInput() + 204
5   rsession                      	0x00000001007b953f rstudio::core::system::file_monitor::detail::run(rstudio_boost::function<void ()> const&) + 47
6   rsession                      	0x0000000100775200 rstudio::core::system::file_monitor::(anonymous namespace)::fileMonitorThreadMain() + 368
7   rsession                      	0x00000001005fde03 rstudio_boost::detail::thread_data<rstudio_boost::function<void ()> >::run() + 35
8   rsession                      	0x00000001008c3080 rstudio_boost::(anonymous namespace)::thread_proxy(void*) + 176
9   libsystem_pthread.dylib       	0x00007fff6854e109 _pthread_start + 148
10  libsystem_pthread.dylib       	0x00007fff68549b8b thread_start + 15

Thread 2:
0   libsystem_kernel.dylib        	0x00007fff68489882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6854e425 _pthread_cond_wait + 698
2   rsession                      	0x00000001008c53cc rstudio_boost::condition_variable::do_wait_until(rstudio_boost::unique_lock<rstudio_boost::mutex>&, timespec const&) + 76
3   rsession                      	0x00000001008c3e0e rstudio_boost::this_thread::hidden::sleep_until(timespec const&) + 78
4   rsession                      	0x0000000100118778 void rstudio_boost::this_thread::sleep<rstudio_boost::date_time::subsecond_duration<rstudio_boost::posix_time::time_duration, 1000ll> >(rstudio_boost::date_time::subsecond_duration<rstudio_boost::posix_time::time_duration, 1000ll> const&) + 536
5   rsession                      	0x0000000100109720 (anonymous namespace)::detectParentTermination() + 32
6   rsession                      	0x00000001005fde03 rstudio_boost::detail::thread_data<rstudio_boost::function<void ()> >::run() + 35
7   rsession                      	0x00000001008c3080 rstudio_boost::(anonymous namespace)::thread_proxy(void*) + 176
8   libsystem_pthread.dylib       	0x00007fff6854e109 _pthread_start + 148
9   libsystem_pthread.dylib       	0x00007fff68549b8b thread_start + 15

Thread 3:
0   libsystem_kernel.dylib        	0x00007fff6848f0fe __select + 10
1   rsession                      	0x00000001000867d1 rstudio_boost::asio::detail::select_reactor::run(bool, rstudio_boost::asio::detail::op_queue<rstudio_boost::asio::detail::task_io_service_operation>&) + 1057
2   rsession                      	0x00000001000860cc rstudio_boost::asio::detail::task_io_service::do_run_one(rstudio_boost::asio::detail::scoped_lock<rstudio_boost::asio::detail::posix_mutex>&, rstudio_boost::asio::detail::task_io_service_thread_info&, rstudio_boost::system::error_code const&) + 556
3   rsession                      	0x0000000100085b18 rstudio_boost::asio::detail::task_io_service::run(rstudio_boost::system::error_code&) + 184
4   rsession                      	0x00000001005afbf9 rstudio_boost::asio::io_service::run() + 41
5   rsession                      	0x00000001008c3080 rstudio_boost::(anonymous namespace)::thread_proxy(void*) + 176
6   libsystem_pthread.dylib       	0x00007fff6854e109 _pthread_start + 148
7   libsystem_pthread.dylib       	0x00007fff68549b8b thread_start + 15

Thread 4:
0   libsystem_kernel.dylib        	0x00007fff68489882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6854e425 _pthread_cond_wait + 698
2   rsession                      	0x000000010001507c bool rstudio_boost::condition_variable_any::do_wait_until<rstudio_boost::unique_lock<rstudio_boost::mutex> >(rstudio_boost::unique_lock<rstudio_boost::mutex>&, timespec const&) + 76
3   rsession                      	0x0000000100014c00 rstudio::session::ClientEventQueue::waitForEvent(rstudio_boost::posix_time::time_duration const&) + 576
4   rsession                      	0x000000010001e0ae rstudio::session::ClientEventService::run() + 1342
5   rsession                      	0x00000001008c3080 rstudio_boost::(anonymous namespace)::thread_proxy(void*) + 176
6   libsystem_pthread.dylib       	0x00007fff6854e109 _pthread_start + 148
7   libsystem_pthread.dylib       	0x00007fff68549b8b thread_start + 15

Thread 5:
0   libsystem_pthread.dylib       	0x00007fff68549b68 start_wqthread + 0

Thread 6:
0   libsystem_pthread.dylib       	0x00007fff685495ad pthread_mutex_lock + 0
1   rsession                      	0x00000001000166d6 rstudio_boost::mutex::lock() + 22
2   rsession                      	0x0000000100810934 rstudio::r::session::ConsoleActions::add(int, std::string const&) + 52
3   rsession                      	0x0000000100129c11 rstudio::session::module_context::consoleWriteError(std::string const&) + 49
4   rsession                      	0x000000010079d8d1 rstudio::core::system::(anonymous namespace)::readFromPipe(int, rstudio_boost::function<void (std::string const&)> const&) + 177
5   rsession                      	0x000000010079d358 rstudio::core::system::(anonymous namespace)::standardStreamCaptureThread(int, rstudio_boost::function<void (std::string const&)> const&, int, rstudio_boost::function<void (std::string const&)> const&) + 296
6   rsession                      	0x00000001008c3080 rstudio_boost::(anonymous namespace)::thread_proxy(void*) + 176
7   libsystem_pthread.dylib       	0x00007fff6854e109 _pthread_start + 148
8   libsystem_pthread.dylib       	0x00007fff68549b8b thread_start + 15

Thread 7:
0   libsystem_kernel.dylib        	0x00007fff68489882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6854e425 _pthread_cond_wait + 698
2   rsession                      	0x0000000100538564 void rstudio_boost::condition_variable_any::wait<rstudio_boost::unique_lock<rstudio_boost::mutex> >(rstudio_boost::unique_lock<rstudio_boost::mutex>&) + 68
3   rsession                      	0x000000010053815a rstudio::core::thread::ThreadsafeQueue<std::string>::wait(rstudio_boost::posix_time::time_duration const&) + 74
4   rsession                      	0x0000000100514262 rstudio::session::modules::rmarkdown::notebook::(anonymous namespace)::NotebookQueue::consoleThreadMain() + 530
5   rsession                      	0x00000001005fde03 rstudio_boost::detail::thread_data<rstudio_boost::function<void ()> >::run() + 35
6   rsession                      	0x00000001008c3080 rstudio_boost::(anonymous namespace)::thread_proxy(void*) + 176
7   libsystem_pthread.dylib       	0x00007fff6854e109 _pthread_start + 148
8   libsystem_pthread.dylib       	0x00007fff68549b8b thread_start + 15

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x0000000101d78dc0  rcx: 0x00007ffeefbf0448  rdx: 0x0000000000000000
  rdi: 0x0000000000000307  rsi: 0x0000000000000006  rbp: 0x00007ffeefbf0470  rsp: 0x00007ffeefbf0448
   r8: 0x0000000000008001   r9: 0x0000000113557200  r10: 0x0000000101d78dc0  r11: 0x0000000000000246
  r12: 0x0000000000000307  r13: 0x00007ffeefbf0660  r14: 0x0000000000000006  r15: 0x0000000000000016
  rip: 0x00007fff6848d33a  rfl: 0x0000000000000246  cr2: 0x000000010cb2a220
  
Logical CPU:     0
Error Code:      0x020000b8
Trap Number:     133

[kevinushey]

0   libsystem_kernel.dylib        	0x00007fff6848d33a __pthread_kill + 10
1   libsystem_pthread.dylib       	0x00007fff6854de60 pthread_kill + 430
2   libsystem_c.dylib             	0x00007fff68414808 abort + 120
3   libomp.dylib                  	0x0000000119bbe69b __kmp_abort_process + 43
4   libomp.dylib                  	0x0000000119bbcdfa __kmp_fatal + 170
5   libomp.dylib                  	0x0000000119bc6385 __kmp_register_library_startup() + 645
6   libomp.dylib                  	0x0000000119bbd4ef __kmp_do_serial_initialize() + 31
7   libomp.dylib                  	0x0000000119bbd4af __kmp_get_global_thread_id_reg + 95
8   libomp.dylib                  	0x0000000119c0f2d9 omp_in_parallel + 9
9   libopenblasp-r0.3.10.dylib    	0x00000001159908cb cblas_dsyrk + 459
10  _multiarray_umath.cpython-36m-darwin.so	0x000000011585280f syrk + 591
11  _multiarray_umath.cpython-36m-darwin.so	0x0000000115852464 cblas_matrixproduct + 4340
12  _multiarray_umath.cpython-36m-darwin.so	0x0000000115680670 PyArray_MatrixProduct2 + 240
13  _multiarray_umath.cpython-36m-darwin.so	0x000000011568bce5 array_matrixproduct + 181
14  libpython3.6m.dylib           	0x0000000115271bdb PyCFunction_Call + 59
15  libpython3.6m.dylib           	0x00000001152129f8 PyObject_Call + 168
16  _multiarray_umath.cpython-36m-darwin.so	0x00000001155c82ba array_implement_array_function + 298

Based on the crash report, it looks like the issue here might be cause by the use of OpenMP / a parallel OpenBLAS. You might need to switch to using a serial OpenBLAS implementation instead.